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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    The journal of ethics 3 (1999), S. 51-71 
    ISSN: 1572-8609
    Keywords: biotechnology ; cloning ; ethics of biotechnology ; ethics of cloning ; ethics of human cloning ; ethics for reproductive technology ; genetic engineering ; human cloning ; religious ethics ; reproductive technology ; secular ethics ; social ethics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Philosophy
    Notes: Abstract The advent of cloning animals has created a maelstrom of social concern about the “ethical issues” associated with the possibility of cloning humans. When the “ethical concerns” are clearly examined, however, many of them turn out to be less matters of rational ethics than knee-jerk emotion, religious bias, or fear of that which is not understood. Three categories of real and spurious ethical concerns are presented and discussed: 1) that cloning is intrinsically wrong, 2) that cloning must lead to bad consequences, and 3) that cloning harms the organism generated. The need for a rational ethical framework for discussing biotechnological advances is presented and defended.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-9368
    Keywords: low molecular weight glutenin promoter ; particle bombardment ; transgene expression ; Triticum aestivum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Transgenic wheat plants from specific cultivars can now be routinely engineered in many laboratories. However, our understanding of the factors controlling transgene expression and stability in wheat compared to other cereals is rather limited. Only a few promoters have been tested in transgenic wheat, and relatively little is known of their relative activities and expression parameters. In the present study, the spatial and temporal properties of one heterologous constitutive promoter and one seed‐specific wheat promoter were investigated. We generated constructs with the reporter gene gusA (β‐glucuronidase) driven by: (a) the constitutive maize ubiquitin‐1 (ubi‐1) promoter, and (b) two different‐sized fragments of the seed‐specific low molecular weight glutenin (LMWG1D1) promoter from wheat. The activities of all three promoter constructs were comparable in endosperm tissue. A detailed analysis of spatial and temporal properties of the promoters is described. Heat shock treatment of transgenic plants carrying the ubi‐1: gusA construct resulted in a significant elevation in the levels of GUS activity. The inheritance of transgene expression levels and stability was evaluated over four generations, as a function of transgene integration patterns and copy number.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1572-9788
    Keywords: transgenic carnation ; genetic engineering ; microprojectile bombardment ; stable transformation ; kanamycin selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Highly efficient Agrobacterium-mediated transformation of carnation (Dianthus caryophyllus L.) was obtained by first wounding stem explants via microprojectile bombardment. When this was followed by cocultivation with disarmed Agrobacterium in the dark, the transformation frequency-based on transient GUS expression-increased to over 10-fold that of explants wounded by other means and cocultivated under constant light. Two cycles of regeneration/selection on kanamycin were employed to generate stably transformed carnation plants and eliminate chimeras: first, plantlets were regenerated from inoculated stem explants and then leaves from these plantlets were used to generate transgenes in a second selection cycle of adventitious shoot regeneration. Agrobacterium strain AGLO, carrying the binary vector pCGN7001 containing uidA and nptII genes, was used in the stable transformation experiments. The combination of wounding via bombardment, cocultivation in the dark and two cycles of kanamycin selection yielded an overall transformation efficiency of 1–2 transgenes per 10 stem explants for the three carnation varieties analyzed. Histochemical and molecular analyses of marker genes in T0 and T1 generations confirmed the transgenic nature of the selected plants.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1572-9788
    Keywords: Basmati 370 and M7 varieties ; δ-endotoxins (Cry1Ac and Cry2A) ; particle bombardment ; snowdrop lectin (GNA) ; transgenic rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract We cotransformed indica rice (Oryza sativa L. cvs. Basmati 370 and M7) with three plasmids, carrying a total of four genes, by particle bombardment. The Bacillus thuringiensis (Bt) δ-endotoxin genes cry1Ac and cry2A were carried on separate vectors, while the gna (snowdrop lectin) and hpt (hygromycin phosphotransferase) genes were linked on the same, cointegrate vector. We evaluated the molecular and expression profiles of 29 independently derived transgenic lines over two generations. The gna and hpt genes cointegrated with a frequency of 100% as expected. Furthermore, 60% of the transgenic plants carried all four genes. Southern blot analysis showed that transgene copy number ranged from 1 to 15. We used western blots to determine protein expression levels in R0 and R1 plants. We observed wide variation in the expression levels of the nonselected transgenes among independently-derived lines, but expression levels within lines derived from the same clone were similar. Consistent with previous reports, we observed no correlation between transgene copy number and the level or stability of protein expression. We show that the introduction of multiple agronomically valuable genes into the rice genome by cotransformation is a practical strategy for engineering elite rice varieties.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1573-5028
    Keywords: enhancer ; flavonoids ; particle bombardment ; pericarp ; promoter ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The maize P-rr gene conditions floral-specific flavonoid pigmentation, especially in the kernel pericarp and cob. We analyzed the P-rr promoter by transient expression assays, in which segments of the P-rr promoter were fused to the GUS reporter gene and introduced into maize cells by particle bombardment. A basal P-rr promoter fragment (−235 to +326) gave low, but significant, levels of GUS reporter gene expression. Interestingly, two widely spaced segments containing enhancer-like activity were found. When tested individually, both the proximal (−1252 to −236) and distal (−6110 to −4842) segments boosted expression of the basal P-rr promoter::GUS construct about five-fold. A 1.6 kb segment of the P-rr promoter (−1252 to +326) containing the proximal enhancer and the 5′-untranslated leader driving the GUS reporter gene showed preferential expression in BMS and embryogenic suspension cell cultures vs. endosperm-derived suspension cell cultures. These results demonstrate the application of transient assay techniques for the identification of regulatory elements responsible for floral-specific regulation of the complex P-rr gene promoter in maize.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1573-5028
    Keywords: genetic engineering ; 4-hydroxybenzoic acid glucoside ; Lithospermum erythrorhizon ; menisdaurin ; shikonin ; ubiC
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The biosynthetic pathway to 4-hydroxybenzoate (4HB), a precursor of the naphthoquinone pigment shikonin, was modified in Lithospermum erythrorhizon hairy root cultures by introduction of the bacterial gene ubiC. This gene of Escherichia coli encodes chorismate pyruvate-lyase (CPL), an enzyme that converts chorismate into 4HB and is not normally present in plants. The ubiC gene was fused to the sequence for a chloroplast transit peptide and placed under control of a constitutive plant promoter. This construct was introduced into L. erythrorhizon by Agrobacterium rhizogenes-mediated transformation. The resulting hairy root cultures showed high CPL activity. 4HB produced by the CPL reaction was utilized for shikonin biosynthesis, as shown by in vivo inhibition of the native pathway to 4HB with 2-aminoindan-2-phosphonic acid (AIP), an inhibitor of phenylalanine ammonia-lyase. A feeding experiment with [1,7-13C2]shikimate showed that in the absence of AIP the artificially introduced CPL reaction contributed ca. 20% of the overall 4HB biosynthesis in the transgenic cultures. ubiC transformation did not lead to a statistically significant increase of shikonin formation, but to a 5-fold increase of the accumulation of menisdaurin, a nitrile glucoside which is presumably related to aromatic amino acid metabolism.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1573-5028
    Keywords: cellulase ; heterologous expression ; Hordeum vulgare L. ; particle bombardment ; thermotolerant endo-1.4-β-glucanase ; transgenic barley
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The malting quality of two barley cultivars, Kymppi and Golden Promise, was modified to better meet the requirements of the brewing process. The egl1 gene, coding for fungal thermotolerant endo-1,4-β-glucanase (EGI, cellulase), was transferred to the cultivars using particle bombardment, and transgenic plants were regenerated on bialaphos selection. Integration of the egl1 gene was confirmed by Southern blot hybridization. The transgenic seeds were screened for the expression of the heterologous EGI. Under the high-pI α-amylase promoter, the egl1 gene was expressed during germination. The heterologous enzyme was thermotolerant at 65 °C for 2 h, thus being suitable for mashing conditions. The amount of heterologous EGI produced by the seeds (ca. 0.025% of soluble seed protein), has been shown to be sufficient to reduce wort viscosity by decreasing the soluble β-glucan content. A decrease in the soluble β-glucan content in the wort improves the filtration rate of beer.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1573-5060
    Keywords: gus expressing cells ; histological analysis ; japonica and indica rice ; particle bombardment ; primary callus ; regeneration capacity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The microprojectile bombardment procedure has allowed the stable transformation of indica and japonica rice varieties, although at different frequencies of transformation depending mainly on their regeneration capacity and on the specific parameters of the transformation protocol. A study of the process of regeneration to whole plants from primary calli derived from mature indica and japonica rice seeds, via embryogenesis, has shown that somatic embryos are produced by division and differentiation of the external cell layers of callus tissues. Adjusting the bombardment conditions to optimize gene delivery to those regenerable cells, we have evaluated the influence of parameters such as the target distance, particle penetration and the effect of osmotic treatment on the regeneration capacity of bombarded cells.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Photosynthesis research 60 (1999), S. 29-42 
    ISSN: 1573-5079
    Keywords: enzyme catalysis ; evolution ; genetic engineering ; photosynthesis ; protein assembly ; protein degradation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39) has played a central role in our understanding of chloroplast biogenesis and photosynthesis. In particular, its catalysis of the rate-limiting step of CO2 fixation, and the mutual competition of CO2 and O2 at the active site, makes Rubisco a prime focus for genetically engineering an increase in photosynthetic productivity. Although it remains difficult to manipulate the chloroplast-encoded large subunit and nuclear-encoded small subunit of crop plants, much has been learned about the structure/function relationships of Rubisco by expressing prokaryotic genes in Escherichia coli or by exploiting classical genetics and chloroplast transformation of the green alga Chlamydomonas reinhardtii. However, the complexity of chloroplast Rubisco in land plants cannot be completely addressed with the existing model organisms. Two subunits encoded in different genetic compartments have coevolved in the formation of the Rubisco holoenzyme, but the function of the small subunit remains largely unknown. The subunits are posttranslationally modified, assembled via a complex process, and degraded in regulated ways. There is also a second chloroplast protein, Rubisco activase, that is responsible for removing inhibitory molecules from the large-subunit active site. Many of these complex interactions and processes display species specificity. This means that attempts to engineer or discover a better Rubisco may be futile if one cannot transfer the better enzyme to a compatible host. We must frame the questions that address this problem of chloroplast-Rubisco complexity. We must work harder to find the answers.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1573-6776
    Keywords: β-glucuronidase ; Catharanthus roseus ; genetic transformation ; green fluorescent protein ; particle bombardment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract In vitro propagation of Catharanthus roseus was achieved using nodal explants. Bud induction was best on medium containing 1.0 mg benzyl aminopurine l−1. Hardening of rooted shoots to soil was very successful with 98% survival. Genetically transformed C. roseus plantlets were obtained after bombardment of nodal explants, which were then micropropagated, with DNA coated particles with green fluorescent protein (GFP) or β-glucuronidase (GUS) reporter genes. Histological studies showed that the gene insertion method proved effective with many cells and different tissues displaying the reporter gene signals, showing that gene expressions were rather stable.
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  • 11
    ISSN: 1573-9368
    Keywords: Antirrhinum ; Arabidopsis ; green fluorescent protein (GFP) ; in vitro ; microspores ; particle bombardment ; tobacco
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The transient expression of three mutant forms of green fluorescent protein (GFP) genes, GFP4, GFP5ER, and GFP4S65C, under several constitutive and pollen‐specific promoters throughout pollen development in Nicotianatabacum, thaliana and Antirrhinummajus is described. Immature pollen of tobacco, Arabidopsis and snapdragon, isolated at different developmental stages, were bombarded with plasmids containing the GFP and cultured in vitro for several days until maturity. The expression of GFP was monitored every day during in vitro maturation, germination and pollination, as well as after in situ pollination. The expression pattern of each construct was compared in parallel experiments to that of ß‐glucuronidase (GUS) constructs expressed by the same promoters. The results show that the expression level of all three GFP mutant forms was dependent on the strength of the promoter used. The strongest promoter was the DC3 promoter, and no notable differences in the intensity and brightness of all three versions of GFP were observed. GFP‐expressing pollen from tobacco and snapdragon developed in vitro for several days until maturity and germinated in vitro as well as on the surface of stigmata, strongly suggesting that all three GFPs are not toxic for the development of functional pollen. Furthermore, stably transformed tobacco plants expressing GFP under the control of the strong pollen‐expressed DC3 and LAT52 promoters were not impaired in reproductive function, confirming that GFP can be used as a non‐destructive marker for plant reproductive biology and development.
    Type of Medium: Electronic Resource
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  • 12
    ISSN: 1573-9368
    Keywords: Oryza sativa ; particle bombardment ; transformation ; transgenic rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We developed a practical and efficient gene transfer system for indica rice utilizing mature-seed derived explants and a simple bombardment device which uses compressed helium for accelerating DNA-coated metal particles. Unlike instruments which have been described in the literature previously, this new bombardment device, which is an improvement of the particle inflow concept, does not require vacuum. This attribute simplifies the transformation procedure significantly and it makes rice transformation technology accessible to laboratories which may not have the resources to invest in more expensive particle bombardment instruments. We determined experimentally that we could recover transgenic rice plants utilizing three different particle bombardment instruments at comparable frequencies.
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  • 13
    ISSN: 1573-9368
    Keywords: particle bombardment ; transgene expression ; Triticum aestivum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A population of R0 transgenic wheat plants, generated by particle bombardment, was analyzed to define molecular, genetic and phenotypic properties resulting from transformation with a cointegrate vector, or cotransformation with two separate plasmids. By evaluating the progeny of 70 independently-derived transgenic plants, we also identified rare events such as chimerism and transgene elimination, which provide valuable information concerning the development of transgenic cereal plants following bombardment experiments. The frequency of chimerism in our transgenic wheat plants was very low. Furthermore, while transgene elimination did occur, this was also a very rare event. We determined the copy numbers of integrated transgenes and the levels of transgene expression. Comparisons to transgenic rice plants generated in the same manner demonstrated some similarities, but also important differences in transgene behavior. Whereas in rice there is no evidence for any direct relationship between transgene copy number and transgene expression or stability, multicopy populations in wheat demonstrated a bias towards higher levels of expression for the two genes and the maize ubiquitin promoter evaluated in the present study.
    Type of Medium: Electronic Resource
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  • 14
    ISSN: 1572-9788
    Keywords: transgenic rice ; particle bombardment ; cell electroporation ; RAPD ; AFLP ; AFRP ; RAMP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In the present work we utilised some of the most discriminative molecular tools, such as RAPD, AFLP, AFRP and RAMP, to analyse the genome of independently derived transgenic plants from three elite Italian cultivars (cv. Lido, Carnaroli and Thaibonnet) and found that two methods for direct gene transfer, namely particle bombardment and intact cell electroporation (the latter being a procedure set up in this work), result in transgenic rice (Oryza sativa L.) plants that exhibit negligible genomic changes. This is in contrast with recently published results showing relevant changes in the DNA of transgenic rice plants generated through protoplasts electroporation and of transgenic poplar plants engineered through Agrobacterium tumefaciens infection. Implications of these findings are discussed in the context of selecting appropriate gene transfer methodologies to produce transgenic plants expressing genes of interest while retaining their genomic integrity and, thus, their superior agronomic and/or industrial traits.
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  • 15
    ISSN: 1572-9788
    Keywords: Bacillus thuringiensis (Bt) ; cry2A ; particle bombardment ; rice leaf folder ; transgenic rice ; yellow stem borer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Transgenic rice indica varieties Basmati 370 and M 7 expressing the novel cry2A (Bt) insecticidal gene were generated by particle bombardment. Molecular and biochemical analyses in R0 and R1 populations confirmed stable integration and expression of this novel Bt transgene. We estimated that the gene product was expressed up to 5% of total leaf protein. Insect feeding bioassays demonstrated that the Cry2A protein was effective against the yellow stem borer and the rice leaf folder, two major rice pests in the Indian Subcontinent. This is the first report of the control of major rice pests using this specific Bt gene. The cry2A gene can now be used in combination with other insecticidal genes for pyramiding resistance against insect pests. This will delay, or perhaps in combination with integrated pest management practices, prevent evolution of insect populations resistant to single insecticidal genes.
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  • 16
    ISSN: 1572-9788
    Keywords: chitinase ; Diplocarpon rosae ; disease resistance ; genetic engineering ; Rosa hybrida L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Blackspot, caused by the Ascomycete fungus Diplocarpon rosae, is the most widespread and pernicious disease of cultivated roses. While some species of rose possess resistance to D. rosae, none of the modern-day rose cultivars are fully resistant to the pathogen. In the current study, Biolistic gene delivery was used to introduce a rice gene, encoding a basic (Class I), chitinase into embryogenic callus of the blackspot-susceptible rose (Rosa hybrida L.) cv. Glad Tidings. The plasmid used for transformation carried the neomycin phosphotransferase (nptII) gene facilitating the selection and regeneration of transgenic plants on medium containing 250 mg/l kanamycin. Southern analysis confirmed integration of 2–6 copies of the chitinase gene into the rose genome; gene expression was confirmed by enzyme assay. Bioassays demonstrated that expression of the chitinase transgene reduced the severity of blackspot development by 13–43%. This degree of resistance to the pathogen correlated with the level of chitinase expression in the transgenic rose plants. The introduction of disease defence genes into rose provides a method of producing blackspot-resistant rose cultivars sought by breeders and growers.
    Type of Medium: Electronic Resource
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  • 17
    ISSN: 1572-9788
    Keywords: BGMV ; common bean ; particle bombardment ; plant transformation ; virus resistance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The genes Rep-TrAP-REn and BC1 from the Brazilian isolate bean golden mosaic geminivirus (BGMV-BR) were cloned in antisense orientation under the transcriptional control of the CaMV 35S promoter. This construct was used to transform common bean (Phaseolus vulgaris L.) using the biolistic method. Transgenic plants from the R3 and R4 generations were challenged by inoculation with a BGMV-BR viruliferous whitefly population. Of the four transgenic lines tested, two had both delayed and attenuated viral symptoms. Un-transformed plants or plants transformed with a construct containing only the gus-neo gene developed typical BGMV-BR symptoms 10–15 days after inoculation.
    Type of Medium: Electronic Resource
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  • 18
    Electronic Resource
    Electronic Resource
    Springer
    Plant molecular biology 38 (1998), S. 1011-1019 
    ISSN: 1573-5028
    Keywords: choline oxidase ; genetic engineering ; glycinebetaine ; low-temperature tolerance ; salt tolerance ; transgenic rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genetically engineered rice (Oryza sativa L.) with the ability to synthesize glycinebetaine was established by introducing the codA gene for choline oxidase from the soil bacterium Arthrobacter globiformis. Levels of glycinebetaine were as high as 1 and 5 μmol per gram fresh weight of leaves in two types of transgenic plant in which choline oxidase was targeted to the chloroplasts (ChlCOD plants) and to the cytosol (CytCOD plants), respectively. Although treatment with 0.15 m NaCl inhibited the growth of both wild-type and transgenic plants, the transgenic plants began to grow again at the normal rate after a significantly less time than the wild-type plants after elimination of the salt stress. Inactivation of photosynthesis, used as a measure of cellular damage, indicated that ChlCOD plants were more tolerant than CytCOD plants to photoinhibition under salt stress and low-temperature stress. These results indicated that the subcellular compartmentalization of the biosynthesis of glycinebetaine was a critical element in the efficient enhancement of tolerance to stress in the engineered plants.
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  • 19
    ISSN: 1573-5060
    Keywords: particle bombardment ; promoter ; tissue-specificity sucrose synthase ; transient expression ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The reporter gene encoding β-glucuronidase (GUS) driven by either of the two maize sucrose synthase gene (Sh1 and Sus 1) promoters was introduced and expressed in various maize tissues via particle bombardment. Transient gene expression was examined by histochemical assays. It was found that the two SS promoters directed differential GUS expression. In the developing kernel, the Sh1 promoter was active only in the upper and central parts of the endosperm. In contrast, strong GUS activity controlled by the Sus1 promoter was detected in various types of cells, including the aleurone cells, the subaleurone endosperm cells, the scutellar cells of the embryo and the pericarp cells. Both promoters showed similar expression patterns in vegetative tissues.
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  • 20
    ISSN: 0006-3525
    Keywords: folding type-specific secondary structure propensities ; amino acids ; α-helical proteins ; β sheet proteins ; α/β proteins ; α+β proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35-49, 1998
    Additional Material: 6 Ill.
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  • 21
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 69-83 
    ISSN: 0006-3525
    Keywords: DNA branched junctions ; branch migration ; superhelical torque ; control of DNA structure ; endonuclease VII ; nanomechanical device ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA branched junctions are analogues of Holliday junction recombination intermediates. Partially mobile junctions contain a limited amount of homology flanking the branch point. A partially mobile DNA branched junction has been incorporated into a synthetic double-stranded circular DNA molecule. The junction is flanked by four homologous nucleotide pairs, so that there are five possible locations for the branch point. Two opposite arms of the branched junction are joined to form the circular molecule, which contains 262 nucleotides to the base of the junction. This molecule represents a system whereby torque applied to the circular molecule can have an impact on the junction, by relocating its branch point. Ligation of the molecule produces two topoisomers; about 87% of the product is a relaxed molecule, and the rest is a molecule with one positive supercoil. The position of the branch point is assayed by cleaving the molecule with endonuclease VII. We find that the major site of the branch point in the relaxed topoisomer is at the maximally extruded position in the relaxed molecule. Upon the addition of ethidium, the major site of the branch point migrates to the minimally extruded position. © 1998 John Wiley & Sons, Inc. Biopoly 45: 69-83, 1998
    Additional Material: 9 Ill.
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  • 22
    ISSN: 0006-3525
    Keywords: conformation ; aggregation ; κ-carrageenan ; flow field-flow fractionation ; multiangle light scattering ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relatively novel combination of flow field-flow fractionation (FFF) and multiangle light scattering (MALS) was employed to study a nondegraded κ-carrageenan in different 0.1M salt solutions. The applicability of the technique was tested, and the effects of salt type and salt composition on the molar mass and radius of gyration were studied. A conformational ordering was induced at room temperature by switching the solvent from 0.1M NaCl (coil form) to 0.1M NaI (helix form). An approximate doubling of the average molar mass and an increase in radius of gyration was then observed, in agreement with results obtained previously using size exclusion chromatography-MALS. This increase in size was attributed to conformational ordering and to the formation of double helices. Severe aggregation was observed above 40% CsI in the 0.1M mixed salt solution of CsI and NaI. This was ascribed to the association of helices into large aggregates. For these large associates, having molar masses of several millions, a reversal of the elution order in flow FFF was detected. © 1998 John Wiley & Sons, Inc. Biopoly 45: 85-96 1998
    Additional Material: 10 Ill.
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  • 23
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 119-133 
    ISSN: 0006-3525
    Keywords: conformations of D-alanyl-D-alanine ; β-lactam ; structural overlay ; AMBER force field ; AM1 ; ab initio ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this article a conformational analysis of the D-alanyl-D-alanine dipeptide, both charged and neutral, has been carried out. The preferred conformations were determined by means of ab initio and semiempirical quantum, together with empirical force field calculations. The AMBER* force field and the 6-31 + G** and 6-31G** ab initio levels give rise to a coincident minimum energy structure, which, on the other hand, differs from that determined by AM1, 3-21 + G, and 3-21G. The solvent effect on the different charged and neutral conformations have been considered through the AMSOL semiempirical method. A quantification regarding the structural similarities between the different dipeptide conformations and the ampicillin has been performed. The results show that the best overlay is attained by the minimum structure energy obtained by using the 6-31 + G** methodology, which presents a planar amidic nitrogen. © 1998 John Wiley & Sons, Inc. Biopoly 45: 119-133, 1998
    Additional Material: 5 Ill.
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  • 24
    ISSN: 0006-3525
    Keywords: chemical oxidation ; cellulose ; conformational transition ; capillary viscosity ; microcalorimetry ; calcium ions ; gels ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational behavior of different molecular weight fractions of a synthetic C6-oxidized derivative of cellulose were investigated by means of capillary viscometry, CD, and microcalorimetric measurements. Experiments were carried out in the presence of either monovalent or divalent counterions.The experimental data indicated that C6-oxidized cellulose can assume an ordered extended conformation at low ionic strength, induced by the intrachain repulsions of negative charges. This conformation was suggested to be very similar to the fully extended structure of cellulose. In addition to this, upon increasing the ionic strength, a conformational transition of the order-to-disorder type occurred. In fact, the screening of the electrostatic repulsions introduced a number of conformational kinks into the cellulosic backbone, which enabled the polymer to assume a more coiled conformation hence producing less viscous aqueous solutions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 157-163, 1998
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  • 25
    ISSN: 0006-3525
    Keywords: conformational stability ; biological polyelectrolytes ; enthalpy ; entropy ; conformational transitions ; carrageenan ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method is proposed for the determination of the enthalpy and entropy changes of nonionic origin upon conformational transition of linear biopolyelectrolytes in solution. For all transition midpoints, defined by given temperature and ionic strength, the total free energy change of the system is zero, which means that the nonionic contribution to the free energy change is equal in value and opposite in sign to the polyelectrolytic one. The counterion condensation theory of linear polyelectrolytes provides for the appropriate analytical expression to be used in such calculations. Linear plots of the proper functions of the calculated free energy changes vs the proper functions of temperature allows for the determination of the enthalpic and entropic terms of the nonionic free energy change of transition.The method has been applied to the extensive available data of the ion-induced conformational change of κ-carrageenan, a linear sulfated galactan extracted from seaweeds. The method has proved very successful, with the results showing a remarkable convergency of the enthalpy values for different monovalent counterions. On the other hand, the above approach has made it possible to explain the known effect of counterion specificity on the transition by a small difference in the nonionic entropic contributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 203-216, 1998
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  • 26
    ISSN: 0006-3525
    Keywords: uv resonance Raman spectroscopy ; Raman cross section ; hypochromism ; DNA ; deoxynucleoside ; protein ; aromatic amino acid ; virus assembly ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ultraviolet resonance Raman (UVRR) spectra of H2O and D2O solutions of the nucleoside (dA, dG, dC, dT) and aromatic amino acid (Phe, Trp, Tyr) constituents of DNA viruses have been obtained with laser excitation wavelengths of 257, 244, 238, and 229 nm. Using the 981 cm-1 marker of Na2SO4 as an internal standard, Raman frequencies and scattering cross sections were evaluated for all prominent UVRR bands at each excitation wavelength. The results show that UVRR cross sections of both the nucleosides and amino acids are strongly dependent on excitation wavelength and constitute sensitive and selective probes of the residues. The results provide a library of UVRR marker bands for structural analysis of DNA viruses and other nucleoprotein assemblies. © 1998 John Wiley & Sons, Inc. Biopoly 45: 247-256, 1998
    Additional Material: 4 Ill.
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  • 27
    ISSN: 0006-3525
    Keywords: hemoglobin ; hexagonal bilayer ; Lumbricus ; electron microscopy ; three-dimensional reconstruction ; small-angle x-ray scattering ; three-dimensional models ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The quaternary structure of Lumbricus terrestris hemoglobin was investigated by small-angle x-ray scattering (SAXS). Based on the SAXS data from several independent experiments, a three-dimensional (3D) consensus model was established to simulate the solution structure of this complex protein at low resolution (about 3 nm) and to yield the particle dimensions. The model is built up from a large number of small spheres of different weights, a result of the two-step procedure used to calculate the SAXS model. It accounts for the arrangement of 12 subunits in a hexagonal bilayer structure and for an additional central unit of cylinder-like shape. This model provides an excellent fit of the experimental scattering curve of the protein up to h = 1 nm-1 and a nearly perfect fit of the experimental distance distribution function p(r) in the whole range. Scattering curves and p(r) functions were also calculated for low-resolution models based on 3D reconstructions obtained by cryoelectron microscopy (EM). The calculated functions of these models also provide a very good fit of the experimental scattering curve (even at h 〉 1 nm-1) and p(r) function, if hydration is taken into account and the original model coordinates are slightly rescaled. The comparison of models reveals that both the SAXS-based and the EM-based model lead to a similar simulation of the protein structure and to similar particle dimensions. The essential differences between the models concern the hexagonal bilayer arrangement (eclipsed in the SAXS model, one layer slightly rotated in the EM model), and the mass distribution, mainly on the surface and in the central part of the protein complex. © John Wiley & Sons, Inc. Biopoly 45: 289-298, 1998
    Additional Material: 4 Ill.
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  • 28
    ISSN: 0006-3525
    Keywords: conformational changes ; vicinal glycosylation ; branched α-l-Rhap(1-2)[β-d-Galp(1-3)]-β-d-Glc1-OMe trisaccharide ; parent disaccharides ; hydrogen bond ; isotope effect ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformations of the α-l-Rhap(1-2)-β-d-Glc1-OMe and β-d-Galp(1-3)-β-d-Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d6 solution by 1H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An “isotopomer-selected NOE” method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular Φ,Ψ-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the Φ,Ψ grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1→2 and 1→3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average Φ,Ψ values of 38°, 17° for the 1→2 and 48°, 1° for the 1→3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues. © 1998 John Wiley & Sons, Inc. Biopoly 46: 417-432, 1998
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  • 29
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    Biopolymers 46 (1998), S. 489-492 
    ISSN: 0006-3525
    Keywords: refractive index increment ; proteins ; solvent ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The refractive index increment of a protein solution is a property not only of the protein, but also of the solvent. This is demonstrated theoretically and confirmed experimentally using analytical interferometry. © 1998 John Wiley & Sons, Inc. Biopoly 46: 489-492, 1998
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  • 30
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    Biopolymers 47 (1998), S. 1-1 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 31
    ISSN: 0006-3525
    Keywords: hepatitis A ; synthetic peptides ; CD ; liposomes ; computational study ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present study was undertaken to examine the structural features that may be important to explain the immunogenicity of the (110-121) peptide sequence (FWRGDLVFDFQV) of VP3 capsid protein of hepatitis A virus. A conformational analysis of the preferred conformations by CD and molecular mechanics was carried out. Present results suggest that the interaction with liposomes as biomembrane model induces and stabilizes the amphipathic β-structure of the peptide.To study the contribution of amino acid replacements at the RGD tripeptide as well as the influence of the peptide chain length on peptide conformation, solid-phase peptide synthesis of several peptide analogs was carried out and the peptide conformation was studied using CD spectroscopy. The results show that the RGD sequence is necessary to induce the β-structure in the presence of liposomes. © 1998 John Wiley & Sons, Inc. Biopoly 45: 479-492, 1998
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  • 32
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    Biopolymers 46 (1998), S. 31-37 
    ISSN: 0006-3525
    Keywords: DNA liquid crystals ; DNA fragments ; screened Coulomb interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The critical volume fractions pertaining to the formation of DNA liquid crystals were obtained from polarization microscopy, 31P-nmr, and phase separation experiments. The DNA length (approximately one to two times the persistence length 50 nm), ionic strength, and counterion variety dependencies are reported. The cholesteric-isotropic transition is interpreted in terms of the coexistence equations, which are derived from the solution free energy including orientational entropy and excluded volume effects. With the wormlike chain as reference system, the electrostatic contribution to the free energy is evaluated as a thermodynamic perturbation in the second virial approximation with a Debye-Hückel potential of mean force. The hard core contribution has been evaluated with scaled particle theory and/or a simple generalization of the Carnahan-Starling equation of state for hard spheres. For sufficiently high ionic strengths, the agreement is almost quantitative. At lower amounts of added salt deviations are observed, which are tentatively attributed to counterion screening effects. The contour length dependence agrees with a DNA persistence length 50 nm. © 1998 John Wiley & Sons, Inc. Biopoly 46: 31-37, 1998
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  • 33
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    Biopolymers 46 (1998), S. 245-252 
    ISSN: 0006-3525
    Keywords: gelatin ; gelation ; atomic force microscopy ; interfacial rheology ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Gelation of gelatin under various conditions has been followed by atomic force microscopy (AFM) with the objective of understanding more fully the structure formed during the gelation process. AFM images were obtained of the structures formed from both the bulk sol and in surface films during the onset of gelation. While gelation occurred in the bulk sol, the extent of helix formation was monitored by measurements of optical rotation, and the molecular aggregation was imaged by AFM. Interfacial gelatin films formed at the air-water interface were also studied. Measurements of surface tension and surface rheology were made periodically and Langmuir-Blodgett films were drawn from the interface to allow AFM imaging of the structure of the interfacial layer as a function of time. Structural studies reveal that at low levels of helical content the gelatin molecules assemble into aggregates containing short segments of dimensions comparable to those expected for gelatin triple helices. With time larger fibrous structures appear whose dimensions suggest that they are bundles of triple helices. As gelation proceeds, the number density of fibers increases at the expense of the smaller aggregates, eventually assembling into a fibrous network. The gel structure appears to be sensitive to the thermal history, and this is particularly important in determining the structure and properties of the interfacial films. © 1998 John Wiley & Sons, Inc. Biopoly 46: 245-252, 1998
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  • 34
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    Biopolymers 48 (1998), S. 65-81 
    ISSN: 0006-3525
    Keywords: nucleotide analogue interference mapping ; phosphorothioate ; group I intron ; interference suppression ; RNA ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I will outline several chemogenetic approaches used to determine the chemical basis of large ribozyme function and structure. The term chemogenetics was first used to describe site-specific functional group modification experiments in the analysis of DNA-protein interactions. Within the past few years equivalent experiments have been performed on large catalytic RNAs using both single-site substitution and interference mapping techniques with nucleotide analogues. While functional group mutagenesis is an important aspect of a chemogenetic approach, chemical correlates to genetic revertants and suppressors must also be realized for the genetic analogy to be intellectually valid and experimentally useful. Several examples of functional group revertants and suppressors have now been obtained within the Tetrahymena group I ribozyme. These experiments define an ensemble of tertiary hydrogen bonds that have made it possible to construct a detailed model of the ribozyme catalytic core. The model includes a functionally important monovalent metal ion binding site, a wobble-wobble receptor motif for helix-helix packing interactions, and a minor groove triple helix. © 1998 John Wiley & Sons, Inc. Biopoly 48: 65-81, 1998
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  • 35
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    Biopolymers 48 (1998), S. 83-96 
    ISSN: 0006-3525
    Keywords: nucleic acid ; disulfide cross-link ; structure ; dynamics ; stability ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids. © 1998 John Wiley & Sons, Inc. Biopoly 48: 83-96, 1998
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  • 36
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    Biopolymers 48 (1998), S. 113-135 
    ISSN: 0006-3525
    Keywords: divalent cations ; magnesium ; RNA ; ion binding ; RNA folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Divalent cations, like magnesium, are crucial for the structural integrity and biological activity of RNA. In this article, we present a picture of how magnesium stabilizes a particular folded form of RNA. The overall stabilization of RNA by Mg2+ is given by the free energy of transferring RNA from a reference univalent salt solution to a mixed salt solution. This term has favorable energetic contributions from two distinct modes of binding: diffuse binding and site binding. In diffuse binding, fully hydrated Mg ions interact with the RNA via nonspecific long-range electrostatic interactions. In site binding, dehydrated Mg2+ interacts with anionic ligands specifically arranged by the RNA fold to act as coordinating ligands for the metal ion. Each of these modes has a strong coulombic contribution to binding; however, site binding is also characterized by substantial changes in ion solvation and other nonelectrostatic contributions. We will show how these energetic differences can be exploited to experimentally distinguish between these two classes of ions using analyses of binding polynomials. We survey a number of specific systems in which Mg2+-RNA interactions have been studied. In well-characterized systems such as certain tRNAs and some rRNA fragments these studies show that site-bound ions can play an important role in RNA stability. However, the crucial role of diffusely bound ions is also evident. We emphasize that diffuse binding can only be described rigorously by a model that accounts for long-range electrostatic forces. To fully understand the role of magnesium ions in RNA stability, theoretical models describing electrostatic forces in systems with complicated structures must be developed. © 1999 John Wiley & Sons, Inc. Biopoly 48: 113-135, 1998
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  • 37
    ISSN: 0006-3525
    Keywords: 1H-nmr ; molecular modeling ; peptaibol ; peptide-lipid interaction ; sodium dodecyl sulfate micelles ; trichorzianin TA VII ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Trichorzianin TA VII, Ac0 U1 A2 A3 U4 J5 Q6 U7 U8 U9 S10 L11 U12 P13 V14 U15 I16 Q17 Q18 Fol19, is a nonadecapeptide member of the peptaibol antibiotics biosynthesized by Trichoderma soil fungi, which is characterized by a high proportion of the α,α-dialkylated amino acids, α-aminoisobutyric acid (Aib, U) and isovaline (Iva, J), an acetylated N-terminus and a C-terminal phenylalaninol (Pheol, Fol). The main interest in such peptides stems from their ability to interact with phospholipid bilayers and form voltage-dependent transmembrane channels in planar lipid bilayers. In order to provide insights into the lipid-peptide interaction promoting the voltage gating, the conformational study of TA VII in the presence of perdeuterated sodium dodecyl sulfate (SDS-d25) micelles has been carried out. 1H sequential assignments have been performed with the use of two-dimensional homo- and -heteronuclear nmr techniques including double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, nuclear Overhauser effect spectroscopy, 1H-13C heteronuclear single quantum correlation, and heteronuclear multiple bond correlation. Conformational parameters, such as 3JNHCαH coupling constants, temperature coefficients of amide protons (Δδ/ΔTNH) and quantitative nuclear Overhauser enhancement data, lead to detailed structural information. Ninety-eight three-dimensional structures consistent with the nmr data were generated from 231 interproton distances and six Φ dihedral angle restraints, using restrained molecular dynamics and energy minimization calculations. The average rms deviation between the 98 refined structures and the energy-minimized average structure is 0.59 Å for the backbone atoms. The structure of trichorzianin TA VII associated with SDS micelles, as determined by these methods, is characterized by two right-handed helical segments involving residues 1-8 and 11-19, linked by a β-turn that leads to an angle about 90°-100° between the two helix axes; residues 18 and 19 at the end of the C-terminal helix exhibit multiple conformations. © 1998 John Wiley & Sons, Inc. Biopoly 46: 75-88, 1998
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  • 38
    ISSN: 0006-3525
    Keywords: 9-hydroxyellipticine ; DNA ; CD ; linear dichroism ; resonance light scattering ; intercalation ; drug-drug interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of 9-hydroxyellipticine to calf thymus DNA, poly[d(A-T)]2, and poly-[d(G-C)]2 has been studied in detail by means of CD, linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the DNA/drug complex are combined with theoretical CD calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the DNA major groove. Analysis of the intercalated binding mode in poly[d(A-T)]2 suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different DNA sequences; however, the stacked binding mode appeared to be more favorable for calf thymus DNA and poly[d(G-C)]2 than for poly[d(A-T)]2, an observation that could be explained by the slightly greater steric hindrance of the poly[d(A-T)]2 major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at DNA : drug mixing ratios of 70:1 the stacked binding mode was still important for GC-rich DNAs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 127-143, 1998
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  • 39
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    Biopolymers 46 (1998), S. 169-179 
    ISSN: 0006-3525
    Keywords: macromolecular carriers ; drug targeting and delivery ; branched chain synthetic polypeptides ; membrane-synthetic polypeptide interaction ; lipid monolayers/bilayers ; polymer therapeutics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The surface properties at the air/water interface and the interaction of branched chain polymeric polypeptides with a general formula poly[Lys-(DL-Alam-X1)], where X = Π (AK), Ser (SAK), or Glu (EAK), with phospholipids were investigated. Polylysine derivatives with polycationic (SAK, AK) or amphoteric (EAK) were capable to spread and form stable monomolecular layers. The stability of monolayers at the air/water interface was dependent on the side-chain terminal amino acid residue of polymers and can be described by SAK 〈 AK 〈 EAK order. The area per amino acid residue values calculated from compression isotherms were in the same range as compared to those of linear poly-α-amino acids and proteins. Moreover, these polymers interact with phospholipid monomolecular layers composed of dipalmitoyl phosphatidyl choline (DPPC) or DPPC/PG (PG: phosphatidyl glycerol; 95/5, mol/mol). Data obtained from compression isotherms of phospholipids spread on aqueous polymer solutions at different initial surface pressure indicated that insertion into lipid monolayers for SAK or AK is more pronounced than for EAK. The interaction between branched polypeptides and phospholipid membranes was further investigated using lipid bilayers with DPPC/PG and fluorescent probes located either at the polar surface [1-(4-trimethylammonium-phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) sodium anilino naphthalene sulfonate (ANS)] or within the hydrophobic core (DPH) of the liposome. Changes in fluorescence intensity and in polarization were observed when TMA-DPH or ANS, but not DPH were used. Comparative data also indicate that all three polymers interact only with the outer surface of the bilayer, but even the most marked penetration of polycationic polypeptide (SAK) did not result in alteration of the ordered state of the alkyl chains in the bilayer. Taken together, data obtained from mono- or bilayer experiments suggest that the interaction between branched polymers and phospholipids are highly dependent on the charge properties (Ser vs Glu) and on the identity (Ser vs Ala) of side-chain terminating amino acids. The binding of polymers to the model membranes could be mainly driven by electrostatic forces, but the significant role of hydrophilic properties in case of SAK cannot be excluded. © 1998 John Wiley & Sons, Inc. Biopoly 46: 169-179, 1998
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  • 40
    ISSN: 0006-3525
    Keywords: Cα,α-dialkylated glycines ; molecular dynamics ; geometry and conformation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between the local backbone conformation and bond angles at Cα of symmetrically substituted Cα,α-dialkylated glycines (Cα,α-dimethylglycine or α-aminoisobutyric acid, Aib; Cα,α-diethylglycine, Deg; Cα,α-di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting flat bottom harmonic potentials, instead of the usual harmonic restraints, for the Cα bond angles. The MD simulations show that the Cα bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-Cα-C′ (τ) angle is the most sensitive conformational parameter and, in the folded form, is always larger and more flexible than in the extended one. © 1998 John Wiley & Sons, Inc. Biopoly 46: 239-244, 1998
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  • 41
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    Biopolymers 46 (1998), S. 319-327 
    ISSN: 0006-3525
    Keywords: methionine ligation ; parathyroid hormones ; biomimetic ligation ; S-methylation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In biological systems, both proteolysis and aminolysis of amide bonds produce activated intermediates through acyl transfer reactions either inter- or intramolecularly. Protein splicing is an illustrative example that proceeds through a series of catalyzed acyl transfer reactions and culminates at an O- or S-acyl intermediate. This intermediate leads to an uncatalyzed acyl migration to form an amide bond in the spliced product. A ligation method mimicking the uncatalyzed final steps in protein splicing has been developed utilizing the acyl transfer amide-bond feature for the blockwise coupling of unprotected, free peptide segments at methionine (Met). The latent thiol moiety of Met can be exploited using homocysteine at the α-amino terminal position of a free peptide for transthioesterification with another free peptide containing an α-thioester to give an S-acyl intermediate. A subsequent, proximity-driven S- to N-acyl migration of this acyl intermediate spontaneously rearranges to form a homocysteinyl amide bond. S-methylation with excess p-nitrobenezensulfonate yields Met at the ligation site. The methionine ligation is selective and orthogonal, and is usually completed within 4 h when performed at slightly basic pH and under strongly reductive conditions. No side reactions due to acylation were observed with any other α-amines of both peptide segments as seen in the synthesis of parathyroid hormone peptides. Furthermore, cyclic peptide can also be obtained through the same strategy by placing both homocysteine at the amino terminus and the thioester at the carboxyl terminus in an unprotected peptide precursor. These biomimetic ligation strategies hold promise for engineering novel peptides and proteins. © 1998 John Wiley & Sons, Inc. Biopoly 46: 319-327, 1998
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  • 42
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    Biopolymers 46 (1998), S. 359-373 
    ISSN: 0006-3525
    Keywords: boundary element method ; DNA electrophoresis ; electrophoretic mobility of DNA ; free solution electrophoretic mobility of DNA ; ion relaxation, DNA electrophoresis ; modeling electrophoresis of polyions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Boundary element methods are used to model the free solution electrophoretic mobility of short DNA fragments. The Stern surfaces of the DNA fragments are modeled as plated cylinders that reproduce translational and rotational diffusion constants. The solvent-accessible and ion-accessible surfaces are taken to be coincident with the Stern surface. The mobilities are computed by solving simultaneously the coupled Navier-Stokes, Poisson, and ion-transport equations. The equilibrium electrostatics are treated at the level of the full Poisson-Boltzmann equation and ion relaxation is included. For polyions as highly charged as short DNA fragments, ion relaxation is substantial. At .11 M KCl, the simulated mobilities of a 20 base pair DNA fragment are in excellent agreement with experiment. At .04 M Tris acetate, pH = 8.0, the simulated mobilities are about 10-15% higher than experimental values and this discrepancy is attributed to the relatively large size of the Tris counterion. The length dependence of the mobility at .11 M KCl is also investigated. Earlier mobility studies on lysozyme are reexamined in view of the present findings. In addition to electrophoretic mobilities, the effective polyion charge measured in steady state electrophoresis and its relationship to the preferential interaction parameter γgG is briefly considered. © 1998 John Wiley & Sons, Inc. Biopoly 46: 359-373, 1998
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  • 43
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    Biopolymers 45 (1998), S. 341-346 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 44
    ISSN: 0006-3525
    Keywords: diffusional encounter ; Brownian dynamics ; average Boltzmann factor ; acetylcholinesterase ; Poisson-Boltzmann ; electrostatics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The utility of the average Boltzmann factor around the active site of an enzyme as the predictor of the electrostatic enhancement of the substrate binding rate is tested on a set of data on wild-type acetylcholinesterase and 18 charge mutants recently obtained by Brownian dynamics simulations. A good correlation between the average Boltzmann factors and the substrate binding rate constants is found. The effects of single charge mutations on both the Boltzmann factor and the substrate binding rate constant are modest, i.e., 〈5 fold increase or decrease. This is consistent with the experimental results of Shafferman et al. but does not support their suggestion that the overall rate of the catalytic reaction is not limited by the diffusional encounter of acetylcholinesterase and its substrate. © 1998 John Wiley & Sons, Inc. Biopoly 45: 355-360, 1998
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  • 45
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    Biopolymers 45 (1998), S. 469-478 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; hydrated proteins ; crystal structures ; density distributions ; globular proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 469-478, 1998
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  • 46
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    Biopolymers 47 (1998), S. 23-29 
    ISSN: 0006-3525
    Keywords: independently folded polypeptide motifs ; miniproteins ; natural target domains ; BBA motif ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we present a redesign strategy for the development of uniquely folded polypeptide motifs of less than 40 residues. These mini proteins are based on natural target domains, including the zinc finger domains (BBA motif) Nomenclature corresponds to the defined elements of secondary structure, beginning at the N-terminus of the peptide. Roman lettering refers to a specific motif while Greek characters correspond to the elements of secondary structure within that motif. and the disulfide-rich snake and scorpion toxins (BBB motif). These motifs are designed to act as the molecular framework for the construction of novel functional polypeptides. We will explore the structural determinants of the folded BBA motif, inspired by the zinc finger peptides, in relation to the redesign process. © 1998 John Wiley & Sons, Inc. Biopoly 47: 23-29, 1998
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  • 47
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    Biopolymers 47 (1998), S. 75-81 
    ISSN: 0006-3525
    Keywords: ion channel ; synthetic peptide ; de novo design ; template-assembled synthetic proteins ; supramolecular assembly ; membrane protein ; planer lipid bilayers ; amphiphilic peptide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To create ion channel function by synthetic peptides is a challenge in the de novo design of artificial membrane proteins. Amphiphilic α-helical motifs of ∼ 20 amino acid residues to span lipid bilayers are most often used for the creation of peptide ion channels. Template molecules to tether helical peptides have been employed to obtain more organized pore structures. Approaches to form molecular assembly of peptides in the membranes by hydrogen bonding have been also investigated. We have developed approaches to assemble helices with individual amino acid sequences to construct artificial helical proteins. Using one of these approaches, four helices corresponding to the voltage sensor segments (S4 in repeat I-IV) of the sodium channel were assembled on a peptide template to give a protein having ion channel activity with rectification. © 1998 John Wiley & Sons, Inc. Biopoly 47: 75-81, 1998
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  • 48
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    Biopolymers 47 (1998), S. 127-142 
    ISSN: 0006-3525
    Keywords: collagen mimetics ; triple helix ; peptoid ; template ; biophysics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Collagen peptidomimetics have been synthesized as an alternative to natural collagen. The incorporation of unnatural residues such as peptoids in the collagen sequences can demonstrate potent and specific biological activity and enhance the biostability against enzymatic degradation. Furthermore, the use of achiral peptoids simplifies synthetic strategies by reducing racemization problems. The peptoid residue N-isobutylglycine (Nleu) has been successfully incorporated into a series of collagen mimetics composed of Gly-Pro-Nleu, Gly-Nleu-Pro, and Gly-Nleu-Nleu. The discovery of template-assembled collagen mimetics and metal binding ability has laid the foundation for new opportunities in the design of novel collagen mimetic complexes. This review summarizes the synthesis and integrated biophysical analyses of the structures of these collagen mimetics. Solid phase segment condensation techniques have been utilized for the synthesis of the single chain and template-assembled analogues. The characterization of the collagen-like structures has been established by temperature-dependent optical rotation measurements, CD, NMR spectroscopy, and molecular modelling simulations. © 1998 John Wiley & Sons, Inc. Biopoly 47: 127-142, 1998
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  • 49
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    Keywords: non-natural amino acid ; peptide ; squarylium dye ; thin film ; poly(3-methylthiophene) ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We designed a polypeptide that behaves as a photodevice by using a non-natural amino acid with replacement of an α-hydrogen by a squarylium dye and succeeded in syntheses of the non-natural amino acid derivative containing a squarylium and its peptide with trialanine Ala-Ala-Ala. Strong dye-dye interactions were confirmed by absorption and CD spectra for the peptide in 2,2,2-trifluoroethanol solution and in water suspension. The non-natural amino acid derivative could be deposited onto a PMeT/Au electrode by the micelle disruption method. © 1998 John Wiley & Sons, Inc. Biopoly 47: 179-183, 1998
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  • 50
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    Biopolymers 47 (1998), S. 263-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 51
    ISSN: 0006-3525
    Keywords: electrostatically driven Monte Carlo method ; cluster analysis ; global energy minimum ; perturbed conformations ; conformational space ; lowest energy conformations ; polypeptide chain ; melittin, membrane-bound portion ; Empirical Conformational Energy Program for Peptides 3 ; annealing methods ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatically driven Monte Carlo (EDMC) method has been greatly improved by adding a series of new features, including a procedure for cluster analysis of the accepted conformations. This information is used to guide the search for the global energy minimum. Alternative procedures for generating perturbed conformations to sample the conformational space were also included. These procedures enhance the efficiency of the method by generating a larger number of low-energy conformations.The improved EDMC method has been used to explore the conformational space of a 20-residue polypeptide chain whose sequence corresponds to the membrane-bound portion of melittin. The ECEPP/3 (Empirical Conformational Energy Program for Peptides) algorithm was used to describe the conformational energy of the chain. After an exhaustive search involving 14 independent runs, the lowest energy conformation (LEC) (-91.0 kcal/mol) of the entire study was encountered in four of the runs, while conformations higher in energy by no more than 1.8 kcal/mol were found in the remaining runs with the exception of one of them (run 8). The LEC is identical to the conformation found recently by J. Lee, H.A. Scheraga, and S. Rackovsky [(1998) “Conformational Analysis of the 20-Residue Membrane-Bound Portion of Melittin by Conformational Space Annealing,” Biopolymers, Vol. 46, pp. 103-115] as the lowest energy conformation obtained in their study using the conformational space annealing method. These results suggest that this conformation corresponds to the global energy minimum of the ECEPP/3 potential function for this specific sequence; it also appears to be the conformation of lowest free energy. © 1998 John Wiley & Sons, Inc. Biopoly 46: 117-126, 1998
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  • 52
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    Biopolymers 46 (1998), S. 195-200 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 53
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    Biopolymers 46 (1998), S. 201-214 
    ISSN: 0006-3525
    Keywords: band broadening ; dispersion ; DNA ; gels ; electrophoresis ; fluorescence recovery ; photobleaching ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We determined quantitatively the band broadening effect during gel electrophoresis by measuring the longitudinal dispersion coefficient Dx, with a fluorescence recovery after photobleaching setup, coupled to an electrophoretic cell. We carried out measurements as a function of the electric field, the average pore size, and the molecular length of DNA fragments. Our results are in good agreement with the predictions of the biased reptation model with fluctuations described by T. A. Duke et al. [(1992) Physics Review Letters, vol. 69, pp. 3260-3263]. This agreement is observed on single-stranded DNA [persistence length ≅ 4 nm; B. Tinland et al. (1997) Macromolecules, vol. 30, pp. 5763-5765] in polyacrylamide gels and on double-stranded DNA (persistence length ≅ 50 nm) in agarose gels, two systems where the ratio between the average pore size and the Kuhn length is larger than 1. © 1998 John Wiley & Sons, Inc. Biopoly 46: 201-214, 1998
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  • 54
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    Biopolymers 46 (1998), S. 403-415 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; DNA curvature ; DNA flexibility ; TATA box functionality ; TATA box binding protein (TBP) ; TBP recognition ; TBP binding ; TBP transcriptional activation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Four 1.5 ns molecular dynamics (MD) simulations were performed on the d(GCTATAAAAGGG) · d(CCCTTTTATAGC) double helix dodecamer bearing the Adenovirus major late promoter TATA element and three iso-composition mutants for which physical and biochemical data are available from the same laboratory. Three of these DNA sequences experimentally induce tight binding with the TATA box binding protein (TBP) and induce high transcription rates; the other DNA sequence induces much lower TBP binding and transcription. The x-ray crystal structures have previously shown that the duplex DNA in DNA-TBP complexes are highly bent. We performed and analyzed MD simulations for these four DNAs, whose experimental structures are not available, in order to address the issue of whether inherent DNA structure and flexibility play a role in establishing these observed preferences. A comparison of the experimental and simulated results demonstrated that DNA duplex sequence-dependent curvature and flexibility play a significant role in TBP recognition, binding, and transcriptional activation. © 1998 John Wiley & Sons, Inc. Biopoly 46: 403-415, 1998
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  • 55
    ISSN: 0006-3525
    Keywords: vibrational CD ; solution conformation ; alanine oligopeptides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution conformation of a number of small, linear alanine oligomers was investigated via ir (or vibrational) CD (VCD). We find that these oligopeptides assume distinct solution conformations that depend primarily on chain lengths, and to a lesser degree on temperature, ionic strength, and pH. As expected, the longer chain oligomers exhibit more distinct VCD features and, presumably, more stable solution structures. At the level of the hexamer, however, aggregation of the peptide occurs. The fast time scale of VCD allows solution structures to be detected that may not be observable using slower techniques such as various forms of nmr spectroscopy. The VCD results reported here confirm that it is generally possible to obtain conformational information for small, linear homo- and heterooligopeptides via VCD spectroscopy. In this respect, the sensitivity of VCD is similar to that of electronic CD. Furthermore, the temperature dependence of the VCD results indicate that at elevated temperatures, the increasing number of conformational states results in a loss of discernible conformers, and consequently, a broadening and weakening of the VCD features. © 1998 John Wiley & Sons, Inc. Biopoly 46: 455-463, 1998
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  • 56
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    Biopolymers 47 (1998), S. 5-22 
    ISSN: 0006-3525
    Keywords: hemoproteins ; model systems ; miniaturized proteins ; mimochromes ; helix structures ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present paper highlights and reviews current research in the field of hemoprotein models. Hemoproteins have been extensively studied in order to understand structure-function relationships, and to design new molecules with desired functions. A wide number of synthetic analogues have been developed, using quite different approaches. They differ in molecular structures, ranging from simple meso-substituted tetraaryl-metalloporphyrins and peptide-porphyrin conjugates.In this paper we summarize the state of the art on peptide based hemoprotein models. We also report here the approach used by us to develop a new class of molecules, named mimochromes. They can be regarded as miniaturized hemoproteins, because mimochromes are low molecular weight compounds with some structural and functional properties common to those of the parent high molecular weight protein. The basic structure of mimochromes is a deuteroporphyrin ring covalently linked to two helical peptide chains. Two molecules of this series have been fully characterized. All the information derived from their structural analysis has been applied to the design of new analogues with additional functions. © 1998 John Wiley & Sons, Inc. Biopoly 47: 5-22, 1998
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  • 57
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    Biopolymers 46 (1998), S. 503-516 
    ISSN: 0006-3525
    Keywords: discrete charge model of DNA ; dielectric cylinder in water ; effective dielectric constant ; salt effects ; Debye shielding factor ; potential variations in DNA surface ; Boltzmann averaged bending angles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied electrostatic properties of DNA with a discrete charge model consisting of a cylindrical dielectric core with a radius of 8 Å and a dielectric constant Di = 4, surrounded by two helical strings of phosphate point charges at 10 Å from the axis, immersed in an aqueous medium with dielectric constant Dw = 78.54. Eliminating the dielectric core makes potentials in the phosphate surface less negative by about 0.5 kT/e. Salt effects are evaluated for the model without a dielectric core, using the shielded Coulomb potential. Smearing the phosphate charges increases their potential by about 2.5 kT/e, due mostly to the self-potential of the smeared charge. Potentials in the center of the minor and major grooves vary less than 0.02 kT/e along their helical path. The potential in the center of the minor groove is from 1.0 to 1.7 kT/e, more negative than in the center of the major groove, depending on dielectric core and salt concentration. So multivalent cations and also larger cationic ligands, such as some antibiotics, are likely to adsorb in the minor groove, in agreement with earlier computations by A. and B. Pullman. Dielectric effects on the surface potential and the local potential variations are found to be relatively small. Bending of DNA is studied by placing a multivalent cation, MZ+, in the center of the minor or major groove, curving DNA around it for a certain length, and calculating the free energy difference between the bent and the straight configuration. Boltzmann averaged bending angles, 〈β〉, are found to be maximal in 0.03M monovalent salt, for a length of about 50 or 25 Å of curved DNA when an MZ+ ion is adsorbed in the minor or the major groove, respectively. When the dielectric constant of water is used throughout the calculation, we find maximal bends of 〈β〉 = 11° for M2+ and 〈β〉 = 16° for M3+ in the minor groove, 〈β〉 = 13° for M3+ in the major groove. The absence of bends in DNA adsorbed to mica in the presence of Mg salts supports the role of Mg2+ in “ion bridging” between DNA and mica. The treatment of the effective dielectric constant between two points outside a dielectric cylinder in water is appended. © 1998 John Wiley & Sons, Inc. Biopoly 46: 503-516, 1998
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  • 58
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    Biopolymers 47 (1998), S. 63-73 
    ISSN: 0006-3525
    Keywords: protein de novo design ; novel macromolecules ; topological templates ; Template Assembled Synthetic Proteins (TASP) ; biosensors ; protein folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ultimate goal in protein de novo design is the creation of novel macromolecules with tailor-made receptor, sensory, and catalytic functions. Despite considerable progress in understanding basic rules of secondary structure formation and protein stability, the well-known protein folding problem is still far from being solved and, in general, only a limited number of designed proteins are folded uniquely. In this article the state-of-the-art in protein design is demonstrated on some selected examples, indicating that the construction of protein-like macromolecules mimicking some essential features of natural proteins seems to be within reach. Thus, protein design and mimicry has become an interdisciplinary challenge with most intriguing perspectives. © 1998 John Wiley & Sons, Inc. Biopoly 47: 63-73, 1998
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  • 59
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    Biopolymers 47 (1998), S. 451-463 
    ISSN: 0006-3525
    Keywords: bacteria ; antibiotics ; linear amphipathic α-helical antimicrobial peptides ; peptide-lipid interactions ; membrane permeation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The increasing resistance of bacteria to conventional antibiotics resulted in a strong effort to develop antimicrobial compounds with new mechanisms of action. Antimicrobial peptides seem to be a promising solution to this problem. Many studies aimed at understanding their mode of action were described in the past few years. The most studied group includes the linear, mostly α-helical peptides. Although the exact mechanism by which they kill bacteria is not clearly understood, it has been shown that peptide-lipid interactions leading to membrane permeation play a role in their activity. Membrane permeation by amphipathic α-helical peptides can proceed via either one of the two mechanisms: (a) transmembrane pore formation via a “barrel-stave” mechanism; and (b) membrane destruction/solubilization via a “carpet-like” mechanism. The purpose of this review is to summarize recent studies aimed at understanding the mode of action of linear α-helical antimicrobial peptides. This review, which is focused on magainins, cecropins, and dermaseptins as representatives of the amphipathic α-helical antimicrobial peptides, supports the carpet-like rather the barrel-stave mechanism. That these peptides vary with regard to their length, amino acid composition, and net positive charge, but act via a common mechanism, may imply that other linear antimicrobial peptides that share the same properties also share the same mechanism. © 1999 John Wiley & Sons, Inc. Biopoly 47: 451-463, 1998
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  • 60
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    Biopolymers 48 (1998), S. 39-55 
    ISSN: 0006-3525
    Keywords: modified nucleotides ; site-specific probes ; RNA structure ; RNA function ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Modified nucleotides can be incorporated site specifically into RNA by the use of total chemical synthesis as well as by use of a variety of recombinant RNA techniques. The range of nucleotide analogues includes modifications to base, sugar, and phosphate for structure-function analysis and for cross-linking studies as well as to answer specific mechanistic questions in RNA catalysis. We describe how RNA containing site-specific modifications are prepared, concentrating in particular on routes involving chemically synthesized oligoribonucleotides, and give examples of their application in studies of the hammerhead and hairpin ribozymes. © 1998 John Wiley & Sons, Inc. Biopoly 48: 39-55, 1998
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  • 61
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    Biopolymers 48 (1998), S. 29-37 
    ISSN: 0006-3525
    Keywords: amide synthase ; catalytic antibodies ; Diels-Alderase ; ideal catalyst platform ; in vitro selection ; Lewis acid ; modified uridines ; modified RNA ; ribozymes ; SELEX ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this manuscript the catalytic ability of RNA is examined and compared to other biopolymers. Despite having considerably fewer catalytically enabling properties when compared to proteins, the power of in vitro selection has allowed for RNA and DNA catalysts to be isolated. RNA catalysis has been expanded by incorporating modified bases to enrich the structural and functional diversity of RNA. Successful examples of new RNA chemistry using base modifications include carbon-carbon bond forming reactions and creation of highly specific active sites that are capable of recognizing small organic molecules without the need for nucleic acid templating or intercalation. In fact, the scope of functional modifications available for use in the RNA platform may eventually surpass those that are found in proteins and there are already hints that well chosen modifications allow nucleic acid catalysts to take advantage of mechanisms not available to selected protein catalysts for similar reactions. The chemical versatility of RNA is just emerging and future research directions will likely entail more creative methods for functional modification that will lead to new catalysts. © 1998 John Wiley & Sons, Inc. Biopoly 48: 29-37, 1998
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  • 62
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    Biopolymers 48 (1998), S. 137-153 
    ISSN: 0006-3525
    Keywords: RNA ; pseudoknot ; Turnip Yellow Mosaic Virus ; Mouse Mammary Tumor Virus ; Beet Western Yellows Virus ; Simian Retrovirus type-1 ; Hepatitis Delta Virus ; translational frameshifting ; ribozyme ; nmr ; x-ray diffraction ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, several high-resolution structures of RNA pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type pseudoknot family. The most complicated pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double pseudoknot. In particular, the structure-function relationships of the H-type pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs. © 1999 John Wiley & Sons, Inc. Biopoly 48: 137-153, 1998
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  • 63
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1-24 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We study the large time asymptotics of solutions u(x, t) of the wave equation with time-harmonic force density f(x)e-iωt, ω≥0, in the semi-strip Ω= (0, ∞)×(0, 1) for a given f∊C∞0(Ω). We assume that u satisfies the initial condition u=(∂/∂t)u=0 for t=0 and the boundary conditions u=0 for x2=0 and x2=1, and (∂/∂x1)u=αu for x1=0, with given α, -π≤α〈∞. Let Dα be the self-adjoint realization of -Δ in Ω with this boundary condition. For -π≤α〈0, Dα has eigenvalues λj=π2j2-α2, j=1, 2, … For j≥2 these eigenvalues are embedded in the continuous spectrum of Dα, σc(Dα)=[π2, ∞]. For α≥0, Dα has no eigenvalues. We consider the asymptotic behaviour of u(x, t), t→∞, as a function of α. In the case α=0 resonances of order √t at ω=πj, j=1, 2, …, were found in References 5 and 10. We prove that for α=-π there is a resonance of order t2 for ω=0 and resonances of order t for every ω〉0 (note that 0 is an eigenvalue of D-π). Moreover, for -π〈α〈0 there are resonances of order t at ω=√λj. The resonance frequencies are continuous functions of α for -π〈α〈0 and tend to πj, j=1, 2, … as α goes to zero.On the contrary in the case α〉0 there are no real resonances in the sense that the solution remains bounded in time as t→∞. Actually in this case, the limit amplitude principle is valid for all frequencies ω≥0. This rather striking behaviour of the resonances is explained in terms of the extension of the resolvent R(κ)=(Dα-κ2)-1 as a meromorphic function of κ into an appropriate Riemann surface. We find that as α crosses zero the real poles of R(κ) associated with the eigenvalues remain real, but go into a second sheet of the Riemann surface. This behaviour under perturbation is rather different from the case of complex resonances which has been extensively studied in the theory of many-body Schrödinger operators where the (real) eigenvalues embedded in the continuous spectrum turn under a small perturbation into complex poles of the meromorphic extension of the resolvent, as a function of the spectral parameter κ2. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 117-128 
    ISSN: 0170-4214
    Keywords: third-grade fluid ; existence ; uniqueness ; classical solution ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The global existence and uniqueness of classical solution of steady motions of a third-grade fluid provided assumptions on positivness of μ (coefficient of viscosity) and α1, γ (material coefficients) is proved. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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  • 65
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 227-249 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Integral equations associated with the basic boundary value problems for the Laplace and Stokes equations are considered. The integral operators for these integral equations are interpreted as the pseudodifferential operators, and their principal symbols are calculated. The symbols are obtained in terms of the principal curvatures and the coefficients of the first quadratic form of the boundary. As a consequence, the initial approximation is suggested for the iterative methods solving the integral equations. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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  • 66
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 327-359 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The boundary integral equation method is used to prove the convergence of the Drude-Born-Fedorov equations with variable coefficients, possibly non-smooth, to Maxwell's equations as chirality admittance tends to zero. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 565-588 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: New explicit stability conditions are derived for a linear integro-differential equation with periodic operator coefficients. The equation under consideration describes oscillations of thin-walled viscoelastic structural members driven by periodic loads. To develop stability conditions two approaches are combined. The first is based on the direct Lyapunov method of constructing stability functionals. It allows stability conditions to be derived for unbounded operator coefficients, but fails to correctly predict the critical loads for high-frequency excitations. The other approach is based on transforming the equation under consideration in such a way that an appropriate ‘differential’ part of the new equation would possess some reserve of stability. Stability conditions for the transformed equation are obtained by using a technique of integral estimates. This method provides acceptable estimates of the critical forces for periodic loads, but can be applied to equations with bounded coefficients only. Combining these two approaches, we derive explicit stability conditions which are close to the Floquet criterion when the integral term vanishes. These conditions are applied to the stability problem for a viscoelastic bar compressed by periodic forces. The effect of material and structural parameters on the critical load is studied numerically. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 653-664 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In order to maintain spectrally accurate solutions, the grids on which a non-linear physical problem is to be solved must also be obtained by spectrally accurate techniques. The purpose of this paper is to describe a pseudospectral computational method of solving integro-differential systems with quadratic performance index. The proposed method is based on the idea of relating grid points to the structure of orthogonal interpolating polynomials. The optimal control and the trajectory are approximated by the m th degree interpolating polynomial. This interpolating polynomial is spectrally constructed using Legendre-Gauss-Lobatto grid points as the collocation points, and Lagrange polynomials as trial functions. The integrals involved in the formulation of the problem are calculated by Gauss-Lobatto integration rule, thereby reducing the problem to a mathematical programming one to which existing well-developed algorithms may be applied. The method is easy to implement and yields very accurate results. An illustrative example is included to confirm the convergence of the pseudospectral Legendre method, and a comparison is made with an existing result in the literature. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 701-718 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This article establishes the existence of a trapped-mode solution to a linearized water-wave problem. The fluid occupies a symmetric horizontal channel that is uniform everywhere apart from a confined region which either contains a thin vertical plate spanning the depth of the channel or has indentations in the channel walls; the forces of gravity and surface tension are operative. A trapped mode corresponds to an eigenvalue of the composition of an inverse differential operator and a Neumann-Dirichlet operator for an elliptic boundary-value problem in the fluid domain. The existence of such an eigenvalue is established by extending previous results dealing with the case when surface tension is absent. © 1998 B.G. Teubner Stuttgart-John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 501-517 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper an initial-boundary-value problem in one-space dimension is studied for the Broadwell model extended to a gas mixture undergoing bimolecular reactions. Techniques of semigroup of bounded positive operators in a suitable Banach space are used to prove existence and uniqueness of the solution on bounded time intervals whose length depends on the initial data. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 685-700 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In the present work, the problem of electromagnetic wave propagation in three-dimensional stratified media is studied. The method of decoupling the electric and magnetic fields is implemented, and the spectral approach is adopted, componentwise, to the vector equation involving the electric field. Operational calculus of self-adjoint, positive operators in suitable Hilbert spaces is used to solve the corresponding initial value problems. The spectral families of these operators for the cases of the whole space and of a finite layer are constructed. A discussion on the applicability of the obtained results to physical problems is also included. © 1998 B.G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 757-780 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we prove under the assumption of small initial data the global existence of a classical solution to the equations in viscoelasticity, associated with a free damping boundary condition. We also show that if we choose the initial data large enough, blow up will occur in finite time. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 797-821 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider the thermoelastic plate system,utt-γΔutt+Δ2u+αΔθ=0,θt-κΔθ-αΔut=0 and we make a comparison between the models in which γ=0 and γ〉0. We conclude that in the first case the plate system is of a parabolic type, while when γ〉0 the corresponding system has a hyperbolic behaviour. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 883-894 
    ISSN: 0170-4214
    Keywords: solitary wave ; stability ; long wave-short wave resonance equations ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This paper concerns the orbital stability for solitary waves of the Long Wave-Short Wave resonance equations. Since the abstract results of Grillakis et al. [7, 8] cannot be applied directly, we can extend the abstract stability theory and use the detailed spectral analysis to obtain the stability of the solitary waves. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1049-1066 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider particle transport in a three-dimensional convex region V, bounded by the regular surface ∂V. We assume that particles are specularly reflected by ∂V and that a source q is assigned on ∂V; more general non-homogeneous boundary conditions are also discussed. The problem is non-linear because the boundary condition is not homogeneous. We prove existence of a unique strict solution and by using the theory of semigroups we derive the explicit expression of such a solution in terms of the boundary source q. In the appendix, we indicate how some properties of affine operators can be used to derive the solution. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1085-1105 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: A phase-field model based on the Coleman-Gurtin heat flux law is considered. The resulting system of non-linear parabolic equations, associated with a set of initial and Neumann boundary conditions, is studied. Existence, uniqueness, and regularity results are proved. An asymptotic analysis is also carried out, in the case where the coefficient of the interfacial energy term tends to 0. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1115-1148 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We apply the Child-Langmuir asymptotics of the Vlasov-Poisson system to the case of a bipolar diode, i.e. a vacuum diode where two species of particles of opposite electric charge are flowing. This leads to a simplified model which, if at least one of the two injected currents is not too large, has a unique solution. Moreover, in that case, the currents flowing inside the diode are limited by the so-called bipolar Child-Langmuir currents. In the case of large currents, other solutions may appear, and the formation of virtual electrodes may occur inside the diode. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1107-1113 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we consider the Cauchy problem for the equation∂u/∂t + u ∂u/∂x + u/x = 0 for x 〉 0, t ≥ 0, with u(x, 0) = u0-(x) for x 〈 x0, u(x, 0) = u0+(x) for x 〉 x0, u0-(x0) 〉 u0+(x0). Following the ideas of Majda, 1984 and Lax, 1973, we construct, for smooth u0- and u0+, a global shock front weak solution u(x, t) = u-(x, t) for x 〈 φ(t), u(x, t) = u+(x, t) for x 〉 φ(t), where u- and u+ are the strong solutions corresponding (respectively) to u0- and u0+ and the curve t → φ(t) is defined by dφ/dt (t) = 1/2[u-(φ(t), t) + u+(φ(t), t)], t ≥ 0 and φ(0) = x0.© 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1195-1206 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: A variational approach to a non-linear non-local identification problem related to the non-linear transport equation is studied. Introducing a similarity transformation, the problem is formulated as an identification problem for a non-linear differential equation of second order with an additional non-local condition. For the solution of the forward problem stability in H1-norm with respect to the identification parameter is obtained. Using this result the existence of a solution to the identification problem is proved. Some results of computational experiments are given. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1233-1267 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider the plate equation in a polygonal domain with free edges. Its resolution by boundary integral equations is considered with double layer potentials whose variational formulation was given in Reference 25. We approximate its solution (u, (∂u/∂n)) by the Galerkin method with approximated spaces made of piecewise polynomials of order 2 and 1 for, respectively, u and (∂u/∂n). A prewavelet basis of these subspaces is built and equivalences between some Sobolev norms and discrete ones are established in the spirit of References 14, 16, 30 and 31. Further, a compression procedure is presented which reduces the number of nonzero entries of the stiffness matrix from O(N2) to O(N log N), where N is the size of this matrix. We finally show that the compressed stiffness matrices have a condition number uniformly bounded with respect to N and that the compressed Galerkin scheme converges with the same rate than the Galerkin one. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1287-1296 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The relativistic Vlasov-Maxwell-Fokker-Planck system is used in modelling distribution of charged particles in plasma. It consists of a transport equation coupled with the Maxwell system. The diffusion term in the equation models the collisions among particles, whereas the viscosity term signifies the dynamical frictional forces between the particles and the background reservoir. In the case of one space variable and two momentum variables, we prove the existence of a classical solution when the initial density decays fast enough with respect to the momentum variables. The solution which shares this same decay condition along with its first derivatives in the momentum variables is unique. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1415-1439 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider reactive mixtures of dilute polyatomic gases in full vibrational non-equilibrium. The governing equations are derived from the kinetic theory and possesses an entropy. We recast this system of conservation laws into a symmetric conservative form by using entropic variables. Following a formalism developed by the authors in a previous paper, the system is then rewritten into a normal form, that is, in the form of a quasilinear symmetric hyperbolic-parabolic system. Using a result of Vol'pert and Hudjaev, we prove local existence and uniqueness of a bounded smooth solution to the Cauchy problem. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1479-1494 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Approximate solutions of the non-linear Boltzmann equation, which have the structure of the linear combination of three global Maxwellians with arbitrary hydrodynamical parameters, are considered. Some sufficient conditions which allow the error between the left- and the right-hand sides of the equation tend to zero, and which are calculated either in the mixed metric or in the pure integral metric, are obtained. The class of the distributions, which minimized this error for the arbitrary Knudsen number, is found. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1519-1542 
    ISSN: 0170-4214
    Keywords: non-hyperbolic systems ; two-phase flows ; dispersion terms ; symmetrization ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The paper considers a system of partial differential equations of convection dispersion type, modelling a stratified two-phase fluid flow. Local existence in time is proved for a sufficiently smooth initial data, given in the set of physically admissible states. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1559-1569 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we study the motion of an elastic conducting wire in a magnetic field. The motion of the conductor induces a current in the wire (Faraday's law) which, in turn produces a force on the wire. We consider the linear equation obtained by linearizing the resulting equations of motion about an equilibrium solution. This is a hyperbolic partial differential equation with a non-local term. We prove existence and uniqueness of a weak solution of an initial-boundary value problem for this equation. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1637-1654 
    ISSN: 0170-4214
    Keywords: generalized Stokes equations ; incompressible flow ; least-squares ; finite element method ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we are concerned with a weighted least-squares finite element method for approximating the solution of boundary value problems for 2-D viscous incompressible flows. We consider the generalized Stokes equations with velocity boundary conditions. Introducing the auxiliary variables (stresses) of the velocity gradients and combining the divergence free condition with some compatibility conditions, we can recast the original second-order problem as a Petrovski-type first-order elliptic system (called velocity-stress-pressure formulation) in six equations and six unknowns together with Riemann-Hilbert-type boundary conditions. A weighted least-squares finite element method is proposed for solving this extended first-order problem. The finite element approximations are defined to be the minimizers of a weighted least-squares functional over the finite element subspaces of the H1 product space. With many advantageous features, the analysis also shows that, under suitable assumptions, the method achieves optimal order of convergence both in the L2-norm and in the H1-norm. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1619-1635 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider the two-parameter non-linear Sturm-Liouville problems. By using the variational method on general level sets, the variational eigenvalues are obtained. The purpose of this paper is to study the properties of these variational eigenvalues with respect to the parameter of general level sets. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 187-226 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We study the limit behaviour of solution of Poisson's equation in a class of thin two-dimensional domains, both simply connected or single-hollowed, as its thickness becomes very small. The method is based on a transformation of the original problem into another posed on a fixed domain, obtention of a priori estimates and convergence results when thickness parameter tends to zero. As an important application of abstract results we obtain the limit expressions for functions appearing in elastic beam theories as torsion and warping functions. In this way, we provide a mathematical justification and a correct definition of torsion, warping and Timoshenko functions and constants that should be used in the open and closed thin-walled elastic beam theories. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 269-279 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The generalized Möbius function and Möbius inversion formula are applied to a multiplicative semigroup. A general mathematical method based on this Möbius inversion is presented to solve inversion problems of expansions with unequally weighted terms. By this method, all the inverse lattice problems in physics can be solved concisely. The solutions of four inverse lattice problems: the Fibonacci structure, the square lattice structure, the bcc and the hcp lattice structures are given. These are difficult to be solved by other methods. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 361-374 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We use the eigenfunction expansion of Green's function of Dirichlet problems to obtain sampling theorems. The analytic properties of the sampled integral transforms as well as the uniform convergence of the sampling series are proved without any restrictions on the integral transforms. We obtain a one- and multi-dimensional versions of sampling theorems. In both cases the sampling series are written in terms of Lagrange-type interpolation expansions. Some examples and the truncation error as well as the stability of the obtained sampling expansions are discussed at the end of the paper. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 393-416 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider a dynamical von Kármán system in the presence of thermal effects. Our model includes the possibility of a rotational inertia term in the system. We show that the total energy of the solution of such system decays exponentially as t→+∞. The decay rates we obtain are uniform on bounded sets of the energy space. The main ingredients of our method of proof are suitable properties of a decoupled system, the energy method and the compactness of the nonlinear map associated to the von Kármán system. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 479-488 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This short article discusses the spectrum of the Neumann Laplacian in the infinite domain Ω⊂∝n, n ≥2 created by inserting a compact obstacle P into the uniform cylinder Ω0 =(-∞, ∞)×Ω′. The main result is the existence of at least one embedded eigenvalue when P is an (n -2)-dimensional surface whose unit normal is parallel to Ω′ at each point of P . The special case when P is symmetric about {0}×Ω′ is also treated. It is shown that there is at least one symmetric eigenvector and, when P is sufficiently long, at least one antisymmetric eigenvector. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 551-564 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We prove the existence of solutions to the three-dimensional elastoplastic problem with Hencky's law and Neumann boundary conditions by elliptic regularization and the penalty method, both for the case of a smooth boundary and of an interior two dimensional crack. It is shown, in particular, that the variational solution satisfies all boundary conditions. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 251-268 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The propagation of Hölder regularity of the solutions to the 3D Euler equations is discussed. Our method is a special semi-linearization of the vorticity equation combined with the classical Schauder interior estimates. © 1998 by B.G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 433-461 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This paper is concerned with the solution of Maxwell equations in the modelling of the scattering of a time-harmonic electromagnetic wave by an obstacle located in a two-layered medium. The use of the Silver-Müller radiation condition in each layer is shown to provide a well-posed scattering problem. The analysis is based on the study of the Green tensor, which allows to relate the radiation condition to an integral representation formula. The analyticity properties of the scattering problem with respect to the frequency are then investigated. This gives rise to a limiting absorption principle and furnishes a characterization of the resonances. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 489-499 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We apply our recently developed distributional technique [2, 3] to study time-domain asymptotics. This enables us to present a rigorous mathematical discussion and extensions of the results given by Chapman [1] and subsequent workers in this field. The present analysis is facilitated by defining functions which are distributionally small at infinity. We find that one of the advantages of using this technique is that multidimensional extensions can be derived very easily. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Type of Medium: Electronic Resource
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  • 97
    Electronic Resource
    Electronic Resource
    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 519-549 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This paper is concerned with a specific finite element strategy for solving elliptic boundary value problems in domains with corners and edges. First, the anisotropic singular behaviour of the solution is described. Then the finite element method with anisotropic, graded meshes and piecewise linear shape functions is investigated for such problems; the schemes exhibit optimal convergence rates with decreasing mesh size. For the proof, new local interpolation error estimates for functions from anisotropically weighted spaces are derived. Finally, a numerical experiment is described, that shows a good agreement of the calculated approximation orders with the theoretically predicted ones. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 98
    Electronic Resource
    Electronic Resource
    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 605-617 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This paper presents a general method of analysis for investigating the whirl stability of a rotor-bearing system whose appendage is flexibly attached to the spinning shaft. Sufficient conditions of asymptotic stability involving system different parameters are derived based on Liapunov's theory. An inclusive analysis of the effect of the combined flexibilities of the elastic attachment of the appendage to the shaft and the two end bearings coupled with the other various parameters of the system on the dynamic stability is presented. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 99
    Electronic Resource
    Electronic Resource
    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 665-684 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We investigate the steady compressible Navier-Stokes equations near the equilibrium state v = 0, ρ = ρ0 (v the velocity, ρ the density) corresponding to a large potential force. We introduce a method of decomposition for such equations: the velocity field v is split into a non-homogeneous incompressible part u (div (ρ0u) = (0) and a compressible (irrotational) part ∇φ. In such a way, the original complicated mixed elliptic-hyperbolic system is split into several ‘standard’ equations: a Stokes-type system for u, a Poisson-type equation for φ and a transport equation for the perturbation of the density σ = ρ - ρ0. For ρ0 = const. (zero potential forces), the method coincides with the decomposition of Novotny and Padula [21]. To underline the advantages of the present approach, we give, as an example, a ‘simple’ proof of the existence of isothermal flows in bounded domains with no-slip boundary conditions. The approach is applicable, with some modifications, to more complicated geometries and to more complicated boundary conditions as we will show in forthcoming papers. © 1998 B.G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 619-651 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider acoustic scattering from an obstacle inside an inhomogeneous structure. We prove in the paper that if the outside inhomogeneity is known then the obstacle and possible inside inhomogeneity are uniquely determined by the fixed energy far field data. The proof is based on new mapping properties of layer potentials in spaces that specify one point. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Type of Medium: Electronic Resource
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